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This article is part of the supplement: APBioNet – Fifth International Conference on Bioinformatics (InCoB2006)

Open Access Proceedings

MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria

Sarita Ranjan1, Ranjit Kumar Gundu2 and Akash Ranjan12*

Author Affiliations

1 Computational & Functional Genomics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India

2 Bioinformatics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India

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BMC Bioinformatics 2006, 7(Suppl 5):S9  doi:10.1186/1471-2105-7-S5-S9

Published: 18 December 2006

Abstract

Background

A key post genomics challenge is to identify how genes in an organism come together and perform physiological functions. An important first step in this direction is to identify transcriptional units, operons and regulons in a genome. Here we implement and report a strategy to computationally identify transcriptional units and operons of mycobacteria and construct a database-MycoperonDB.

Description

We have predicted transcriptional units and operons in mycobacteria and organized these predictions in the form of relational database called MycoperonDB. MycoperonDB database at present consists of 18053 genes organized as 8256 predicted operons and transcriptional units from five closely related species of mycobacteria. The database further provides literature links for experimentally characterized operons. All known promoters and related information is collected, analysed and stored. It provides a user friendly interface to allow a web based navigation of transcription units and operons. The web interface provides search tools to locate transcription factor binding DNA motif upstream to various genes. The reliability of operon prediction has been assessed by comparing the predicted operons with a set of known operons.

Conclusion

MycoperonDB is a publicly available structured relational database which has information about mycobacterial genes, transcriptional units and operons. We expect this database to assist molecular biologists/microbiologists in general, to hypothesize functional linkages between operonic genes of mycobacteria, their experimental characterization and validation. The database is freely available from our website http://www.cdfd.org.in/mycoperondb/index.html webcite.